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Update:
I recovered the backup made before the apt upgrade and the error persists, I had a suspicion that some bot trying to access wp-login is causing this because some times I observed a connection some minutes before the errors starting and blocke on nginx, but still have errors:

The error provided suggests the issue is coming from PHP-FPM. You’ll need to enable the catch_workers_output module. This can be set
on /etc/php5/fpm/pool.d/www.conf. As soon as you do, restart the service and check your php5-fpm.log. Check the log and it should provide more descriptive errors.